This is a revised renewal application for a highly productive Program Project, Biomarkers and Pathogenesis of MS: From Mouse to Human, comprised of three projects, a Statistical Core, an Animal Model/Human Tissue Bank Core and an Imaging Core that are focused on understanding mechanisms of pathogenesis of CNS inflammatory autoimmune disorders, especially multiple sclerosis (MS). Better understanding of the mechanisms of MS progression, and what underlies the continued axonal damage and drop-out would help guide development of new therapeutics for this common disease. Additionally, an urgent need exists for innovative methods to measure CNS inflammation, demyelination and axonal injury, as well as CNS repair, not only to better understand human MS pathogenesis, but also to expedite testing of novel therapeutics. A major innovation was achieved during our first five years with our development of the novel Diffusion Basis Spectrum Imaging (DBSI) which we now propose to definitively validate and carry forward to address current needs. Following encouragement and guidance from initial reviewers, we expanded our prior focus to encompass mechanistic studies of the communication between the invading inflammatory cells and resident cells in the CNS, leading to loss of blood-brain barrier integrity. State-of-the-art imaging modalities will be used. The three P01 projects are linked thematically with the goals of defining the interface between blood-brain barrier signaling and immune cell entry and how this impacts the development of persistent inflammatory lesions, and axonal pathologies. The latter, in particular, may underlie progressive MS. Each project uses all three Cores that provide statistical, animal model/human tissue bank, imaging and administrative support. Overall objectives are to (1) develop and test novel cutting edge noninvasive and specific MRI biomarkers of white matter injuries using animal models, human tissues, and MS patients; and (2) to address and target the mechanisms by which changes in vascular permeability impact leukocyte activation and entry into CNS.